From owner-chemistry@ccl.net Sat Dec 24 19:16:01 2005
From: "Alan Shusterman alan]-[reed.edu" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: Most important recent development in molecular modeling since 2000?
Message-Id: <-30391-051224191429-29151-VPQ63PQ8w2m+P8N+kyPVsw[a]server.ccl.net>
X-Original-From: Alan Shusterman <alan/./reed.edu>
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Date: Sat, 24 Dec 2005 16:13:46 -0800
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Sent to CCL by: Alan Shusterman [alan===reed.edu]
Lingran,

Here are my ideas. Since they don't involve force fields, I'm sure that 
my suggestions will disappoint you:

Thesis: The pursuit of more powerful and more accurate modeling tools 
(both nice to be sure) makes us overlook two aspects of modeling that 
make it meaningful to chemistry as a whole: accessibility to large 
numbers of chemists, and sufficiently easy to use that one can *play* 
with models and ideas. In this spirit, I would say the biggest 
improvements since 2000 have been:

1. spread of powerful, e.g., DFT-based, modeling tools to desktop computers
2. much greater adoption of computer modeling software by textbook 
authors (still a work in progress b/c the authors use only a fraction of 
the software's capabilities, and the teachers use only a fraction of 
what the authors produce)

Happy New Year!
-Alan

William Lingran Chen lchen|*|mdli.com wrote:

>Sent to CCL by: William Lingran Chen [lchen]_[mdli.com]
>Recently Perry post a news "Researchers at Los Alamos National 
>Laboratory have set a new world's record by performing the first 
>million-atom computer simulation in biology." (10/24/2005).
>
>What are other most important progresses in the field of molecular 
>modeling in this century (since 2000)?
>I am most interested in
>
>1. New force fields,
>2. Major improvement of the existing force fields,
>3. New molecular modeling software,
>
>Thanks.
>Lingran>
>
>
>  
>

-- 
Alan Shusterman
Chemistry Department
Reed College
Portland, OR 97202-8199
503-517-7699
http://academic.reed.edu/chemistry/alan/
"Yield and overcome; Bend and be straight." Lao Tzu 22


From owner-chemistry@ccl.net Sat Dec 24 21:38:01 2005
From: "Wenjun Zheng zhengwj:-:helix.nih.gov" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: Announcement of a new web-server for analysing protein dynamics
Message-Id: <-30392-051224204805-26503-O2JaOrffflujykOLamF5fw*o*server.ccl.net>
X-Original-From: "Wenjun  Zheng" <zhengwj:helix.nih.gov>


Sent to CCL by: "Wenjun  Zheng" [zhengwj[]helix.nih.gov]
Dear researchers on protein dynamics:
     The Laboratory of Computational Biology at NHLBI/NIH is
happy to present a new web server (AD-ENM) for analyzing dynamics of
protein structures based on the elastic network model. The server is now
available to public users at http://enm.lobos.nih.gov. So far the
functions of AD-ENM server include:
     1. Describing collective protein conformational changes using
low-frequency normal modes;
     2. Predicting protein conformational changes induced by given local
structural deformations (caused by ligand binding);
     3. Identifying key residues which are dynamically important to a
given functional site.
     The AD-ENM is still under testing. You are very welcome to try it and
report any bugs or drop any comment to me by email
(zhengwj ~~ helix.nih.gov).
     More functions will be added in the future.

     Thank you for your attention!

Wenjun Zheng, PhD
NIH,NHLBI